Mrs. Babs--
Welcome to the forum!
I'm pretty sure that the pagination issue you've seen reference to is that the Sony Software will "pre-paginate" a book before loading it onto the reader. Basically, your computer figures out where the page breaks should be in each font size and then sends that information to the reader. This makes the book load much faster the first time you open it up on your reader or switch font sizes for the first time.
Calibre doesn't have the ability to do this, so when you send a book to the reader with Calibre, the first time you open the book on the reader, it could take awhile while the reader figures out where the page breaks are. Not a big issue once the book is loaded.
As far as I know the only way to load Sony DRM'ed books from the Sony Connect Site is through the Sony Software.
Enjoy your reader!!
dordale